We have made a thorough re-examination of the Rayleigh-Taylor instability in the nighttime equatorial ionosphere from ~100 km to the bottomside F region. We have taken into account explicitly the following effects which have been ignored by other workers in various combinations: (1) The eastward drift of the ionosphere caused by the nighttime polarization electric field, (2) the eastward nighttime neutral wind, and (3) recombination in the F and E regions. We found that, well below the bottomside F region, the Rayleigh-Taylor mode can be unstable and is driven by an eastward neutral wind rather than by gravitational drift. Formation of ionospheric bubbles below the bottomside F region is consistent with the observation of lower ionospheric ions in F region ionospheric holes; furthermore, seasonal and shorter term variations in spread-F occurrence may be associated with variations in the neutral wind and polarization electric field.